/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000150.xml diagram  at 2008.03.20 15:09:39
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000150 extends JavaBaseModel
{

/*
 * Write rules to calculate equation parameters
 */
    private void __internalVarInitFunc_0(double time, double[] x)
    {
        total_fluorescence = x[0]*599990.0*1000000.0/43200.0 + x[1]*599990.0*1000000.0/43200.0 + basal_fluorescence;
    }


/*
 * Write rules to calculate equation parameters excluding internal variables.
 */
    public void __internalRateVarInitFunc_0(double time, double[] x)
    {
        rate_Activation = Activation_kf*(x[0]/geometry)*geometry - Activation_kb*(x[1]/geometry)*geometry;
        rate_Binding = Binding_kf*(x[2]/geometry)*(x[3]/geometry)*geometry - Binding_kb*(x[0]/geometry)*geometry;
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        geometry = 1.0E-12; // initial value of $geometry
        Activation_kb = 0.557; // initial value of Activation_kb
        Activation_kf = 0.813; // initial value of Activation_kf
        Binding_kb = 25.0; // initial value of Binding_kb
        Binding_kf = 1.9E7; // initial value of Binding_kf
        basal_fluorescence = 1.21210648148148; // initial value of basal_fluorescence
        total_fluorescence = 0.138886574074074; // initial value of total_fluorescence
    }

    /*
     * Model variables initial values
     */
    protected double rate_Activation;
    protected double rate_Binding;
    protected double geometry;
    protected double Activation_kb;
    protected double Activation_kf;
    protected double Binding_kb;
    protected double Binding_kf;
    protected double basal_fluorescence;
    protected double total_fluorescence;

    public double[] extendResult(double time,double [] x)
    {
        this.time = time;

        __internalVarInitFunc_0(time, x);

        double[] y = new double[5];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        y[3] = x[3];
        y[4] = total_fluorescence;
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[4];
        this.time = 0.0;
        x[0] = 0.0; // - $"geometry.CDK2cycA"
        x[1] = 0.0; // - $"geometry.CDK2cycA_star_"
        x[2] = 1.0E-19; // - $"geometry.Cdk2"
        x[3] = 4.0E-19; // - $"geometry.CyclinA"

        __internalVarInitFunc_0(time, x);
        __internalRateVarInitFunc_0(time, x);

        return x;
    }

/*
 * code for algebraic rules calculations
 */

/*
 * end of code for algebraic rules calculations
 */

    protected void calculateRates(double time, double[] x)
    {

        __internalVarInitFunc_0(time, x);
        __internalRateVarInitFunc_0(time, x);

    }

        /*
         * calculate dy/dt for 'BIOMD0000000150.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_Activation+rate_Binding;
        result[1] = +rate_Activation;
        result[2] = -rate_Binding;
        result[3] = -rate_Binding;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[4];
        __internalDyDt_0(time, x, result);
        return result;
    }
    public double[] dy_dt(double time, double[] x)
    {
        this.time = time;
        calculateRates( time,x );

        return calculateResult( time,x );
    }

} // class ...